But this is no problem – with P2 you’re in luck: you can always revert to previous configurations:

Help | Software Updates | Installed Software | Revert Configuration

Find and select the configuration using Mylyn 3.0.0, hit Finish, restart Eclipse and you’re done. Thats all you have to do !

… all runs as before 🙂

Some asked why P2 doesn’t remove unused bundles – think its clear now: P2 needs them to be able to revert to older configurations. Did you remember the old days before P2 how much time is costs to fix an update disaster ?